Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
40 Cards in this Set
- Front
- Back
|
What was the first genome to be sequenced completely
|
Haemophilus influenzae
|
|
|
Humans have a lot of _________ while bacteria don't have a lot of them, rather they have a lot of _______
|
introns
extrons |
|
|
Which is the biggest bacteria genome
|
Sorangium cellulosum
|
|
|
What is the range of prokaryotic bp size
|
140 k-13mil
|
|
|
The smallest genomes are ....
|
Obligate symbionts
|
|
|
Buchnera aphidicola
|
Lives in specialized aphid cells (bateriocytes)
Can't repair DNA overproduces amino acids |
|
|
genome reduction is
|
what happens when you become a symbioant. you lose the genes that you don't use. All symbionts undergo gene reduction
|
|
|
Sulcia muelleri and Baumannia cicadellinicola are _______________.
What do each do? |
Leafhopper symbionts.
Sulcia supplies amino acids Baumannia supplies vitamins and cofactors |
|
|
Pelagibacter ubique
|
free-living ( have more than 1 million bp)
|
|
|
biggest genomes are called
|
Myxobateria
|
|
|
This has 13 million base pairs
Displays cellular differentiation Hunt as a pack Can remotely sense objects |
Sorangium cellulosum the boss
|
|
|
What is the human genome project
|
in 1990 wanted to sequence all 3 x 10^9 base pairs of human DNA
completed in 2003 Public effort led by US NHGRI, headed by Francis Collins |
|
|
What is chromosomal walking
|
split genome into fragments then decipher each fragment then put them together
|
|
|
Shotgun sequencing by Craig Venter
|
Blow up DNA into different sizes sequence randomly and find where they overlap
|
|
|
what are Plasmid vectors
|
you can get small DNA fragments of a random DNA you want, put DNA into a plasmid gene and then plasmid will have a selectable marker (like antibiotic resistance). Transform plasmid into E.coli cell for replication. Plasmid is purified to find the sequence of DNA that you inserted
|
|
|
Sequence algorithms used to refine which technique
|
Shotgun sequencing
|
|
|
what is Sangar sequencing
|
basically gel electrophoresis
|
|
|
what does bioinformatics analyse for?
|
genome content , structure, arrangement
|
|
|
what is Open reading frame (ORF)
|
look for a start and stop codon. and the genes in between. That's an ORF. Then you find out what the genes are and what they code for. Proportional to genome size (100 codons)
|
|
|
Gene annotation in ORF
|
Compare ORF sequence to databases
Similar sequence annotated as having similar function Use gene annotations to reconstruct metabolic pathways and determine gene complement |
|
|
ORFs of unknown function are called
|
URF
|
|
|
GENOME MAPS LEARN IT . What's in the outer, second , third , fourth and inside sunburst RINGS
|
Outer circle:
Mbp designation 0 = origin of replication Second ring: Blue: tRNA genes Orange: single rRNA operon Third ring: Dark green: Clockwise ORFs Light green: counterclockwise ORFs Fourth ring: Repetitive DNA: IS elements in orange. They are ssr's (repeted genes that dont code for proteins) Inside sunburst: G+C content: yellow rays = below; orange rays = above 65% |
|
|
The number of ORFs tell us the types of ORFs . How so ? think genome size
|
If the total ORFs small, ie small genome, they have more DNA replication and translation than their other ORFs because these are the essentials.
|
|
|
signal transduction is increases dramatically going from an organism with a __________ genome to a __________ Because this is a more complex behavior and is not essenetial
|
small
Large |
|
|
what is Signal transduction
|
signals other cells
|
|
|
Significant differences in genome content of Bacteria and Archaea are that...
|
Archaea has genes for energy and coenzyme production (also more uncharacterized genes)
Bacteria has genes for carbohydrate metabolism and cytoplasmic membrane functions (transporters) |
|
|
Comparative Genomics
|
Comparing the genome of species with one another and seeing how closely related they are evolution wise.
|
|
|
How can genomes change ? (elementary evolutionary forces)
|
Gene duplication
Gene loss Gene order conservation and rearrangements of genes Nucleotide substitution (recombination + mutation) Horizontal gene transfer |
|
|
In comparative genomic graphs, what do gaps in the coorelation signify ?
|
Deletion in one of the strains
|
|
|
What does an "X" signify on a comparative genomic graph
|
Chromosomal jumping
|
|
|
Can a bacteria's genome grow even larger
|
NOOOO > it has to drop a gene to pick another one up
|
|
|
Evolution by reduction states
|
the loss of pseudogenes not essential for life within the host
|
|
|
Core genome
|
Genes shared by all strains of the same species
|
|
|
Pan genome
|
alll the genes that could be in a group of organisms. Not all organisms in the strain have it
|
|
|
Chromosomal Island
how do you detect it |
They are horizontal transfers
G+C content is different in the transferred bit than the rest |
|
|
What are Pathogenicity islands
|
They encode for virulence factors.
|
|
|
what does -omics mean
|
systematic study
|
|
|
What uses reverse transcriptase and what does it mean? How does it work. TELL ME EVERYTHING
|
enzyme from retrovirus used to produce DNA copies “cDNA” of their genome to integrate into host genome
includes nucleotides, mRNA template molecules, and reverse transcriptase |
|
|
Microarray
|
mRNA reverse trancribed, making a cDNA , that is probed, put onto a microarray to test which part of the DNA is it coorelated to.
Green: expression only in wild-type Red: expression only in mutant Yellow: equivalent expression in both cells |
|
|
Metagenomics is
|
sequencing DNA directly from the enviroment and comparing to known organisms
|
